public void createProteinList() { minProteins = new HashMap<String, Protein>(); for (Peptide pg : minPeptides.values()) { String pepName = pg.getSequence(); for (String protName : pg.getProteins()) { if (minProteins.containsKey(protName)) { Protein prot = minProteins.get(protName); prot.addPeptide(pepName); } else { Protein prot = new Protein(); prot.setName(protName); prot.addPeptide(pepName); prot.setCluster(cluster_num); minProteins.put(protName, prot); } } } for (Protein p : minProteins.values()) { ProteinInfo pInfo = new ProteinInfo(); pInfo.setName(p.getName()); pInfo.setDescription(p.getDescription()); pInfo.setLength(p.getLength()); MassSieveFrame.addProtein(pInfo); } }
public void updateParsimony() { for (Protein prot : minProteins.values()) { for (String pepName : prot.getPeptides()) { Peptide pep = minPeptides.get(pepName); prot.addAssociatedProteins(pep.getProteins()); } } for (Protein prot : minProteins.values()) { prot.updateParsimony(minProteins); } for (Protein prot : minProteins.values()) { prot.computeParsimonyType(); } }
private void addLinkedMembers(PeptideCollection cluster, Integer clustNum, Peptide pg) { for (String proName : pg.getProteins()) { Protein pro = minProteins.get(proName); pro.setCluster(clustNum); for (String pepName : pro.getPeptides()) { Peptide subPg = minPeptides.get(pepName); if (subPg.getCluster() == -1) { subPg.setCluster(clustNum); cluster.addPeptideGroup(subPg); addLinkedMembers(cluster, clustNum, subPg); } } } }
public void updateProteins(HashMap<String, Protein> mainProteins) { minProteins = new HashMap<String, Protein>(); for (Peptide pg : minPeptides.values()) { String pepName = pg.getSequence(); for (String protName : pg.getProteins()) { if (minProteins.containsKey(protName)) { Protein prot = minProteins.get(protName); prot.addPeptide(pepName); } else { Protein prot = mainProteins.get(protName); minProteins.put(protName, prot); } } } for (Peptide pg : minPeptides.values()) { pg.updateProteins(minProteins); } for (Protein p : minProteins.values()) { p.updatePeptides(minPeptides); } }